Atlantic salmon from large Scottish east coast rivers - genetic stock identification: report

Executive summary

Continuing declines in adult Atlantic salmon (Salmo salar) returning to rivers across Scotland have been recorded. The Scottish Wild Salmon Strategy identifies multiple pressures as to the cause of this decline, with climate change a possible contributor as an overall driver, potentially resulting in increased mortality in the marine environment. These declines vary among rivers, possibly because different salmon populations may use the marine environment in different ways. Understanding these differences is important for planning and regulatory purposes, as any riverine differences in migration pathways have the potential to result in stock-specific differences in ecosystem impacts and interactions with offshore developments (e.g. marine renewable energy generation installations). The development of tools to allow insights into stock-specific migration routes is important for conservation efforts and will inform local river managers, recreational and commercial fisheries, as well as both marine renewables and climate change mitigation planning under the Scottish Governments Blue Economy programme for sustainable marine development.

One approach to assess ocean use by salmon is the utilisation of genetic markers to determine the river of origin of salmon captured in the marine environment. This genetic stock identification (GSI) method has become an integral component of modern fisheries management, but requires knowledge of the genetic structure underlying the various populations that make up a stock. Advances in DNA profiling have allowed the development of GSI, resulting, in many cases, in increased geographic resolution and assignment of fish caught at sea to river of origin. In Scotland, although the salmon originating from some individual rivers could be identified using existing GSI protocols, these were the exception. The countrywide resolution that can be achieved using the available genetic markers is limited, in most cases, to regional assignment units that contain a number of neighbouring rivers.

Along the Scottish east coast, the main regional assignment unit stretches from the River Spey to the River Tay and, as such, contains some of the most productive salmon rivers in the country. It would therefore be of significant value to further develop GSI techniques in this region with a view to being able to robustly distinguish between salmon populations from the different rivers within it. This is particularly important to support on-going work using trawled salmon smolts to assess potential impacts of marine renewable energy developments.

Recently, a panel of genetic markers has been developed and successfully utilised in Canada to enhance GSI resolution in the western Atlantic. The aim of this project was to establish the utility of this panel in a Scottish context, focusing on developing the panel along the East coast of Scotland, with a view to determining if the same increase in GSI resolution could be achieved in this important area. To that purpose, 915 juveniles from 40 sites across nine East coast rivers were screened using this marker panel.

Genetic structuring analysis revealed the salmon to be clustered into four distinct groups: the first encompassed the Oykel/Cassley/Shin river system, the second comprised the River Tweed, a third included sites from the Rivers Don and Dee, and the fourth cluster consisted of the remaining east coast sites. Attempts to identify the rivers of origin of fish using this new marker panel revealed poor accuracy at the river level. Increasing accuracy by combining geographically close rivers in a sequential hierarchical process resulted in accurate assignment to three regional units: the Oykel/Cassley/Shin river system, the River Tweed and the largest unit consisting of the remaining screened NE coast rivers. These were similar to the GSI resolution previously obtained with existing marker panels, despite identifying underlying population genetic structuring within the region.